The accuracy of varietal selection using factor analytic models for multi-environment plant breeding trials

Modeling of cultivar x trial effects for multienvironment trials (METs) within a mixed model framework is now common practice in many plant breeding programs. The factor analytic (FA) model is a parsimonious form used to approximate the fully unstructured form of the genetic variance-covariance matrix in the model for MET data. In this study, we demonstrate that the FA model is generally the model of best fit across a range of data sets taken from early generation trials in a breeding program. In addition, we demonstrate the superiority of the FA model in achieving the most common aim of METs, namely the selection of superior genotypes. Selection is achieved using best linear unbiased predictions (BLUPs) of cultivar effects at each environment, considered either individually or as a weighted average across environments. In practice, empirical BLUPs (E-BLUPs) of cultivar effects must be used instead of BLUPs since variance parameters in the model must be estimated rather than assumed known. While the optimal properties of minimum mean squared error of prediction (MSEP) and maximum correlation between true and predicted effects possessed by BLUPs do not hold for E-BLUPs, a simulation study shows that E-BLUPs perform well in terms of MSEP.

Part I. Hydraulics of tidal inlets: simple analytic models for the engineer

Inlets are common coastal features around the world. Essentially an inlet connects a lagoon, a bay or an estuary to the ocean (or sea), and the flow through the inlet channel is primarily induced by the tidal rise and fall of water level in the ocean. When speaking of the hydraulics of an inlet, one is interested mainly in determining the flow through the inlet and the tidal variation in the bay, given the following: (1) Inlet geometry (2) Bay geometry (3) Bottom sediment characteristics in the inlet (4) Fresh water inflow into the bay (and out through the inlet) (5) Ocean tide characteristics A combination of all these factors can produce a rather complex situation. (PDF contains 34 pages.)

Short communication: Principal components and factor analytic models for test-day milk yield in Brazilian Holstein cattle

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Principal components and factor analytic models for birth to mature weights in Nellore cattle

A total of 61,528 weight records from 22,246 Nellore animals born between 1984 and 2002 were used to compare different multiple-trait analysis methods for birth to mature weights. The following models were used: standard multivarite model (MV), five reduced-rank models fitting the first 1, 2, 3, 4 and 5 genetic principal components, and five models using factor analysis with 1, 2, 3, 4 and 5 factors. Direct additive genetic random effects and residual effects were included in all models. In addition, maternal genetic and maternal permanent environmental effects were included as random effects for birth and weaning weight. The models included contemporary group as fixed effect and age of animal at recording (except for birth weight) and age of dam at calving as linear and quadratic effects (for birth weight and weaning weight). The maternal genetic, maternal permanent environmental and residual (co)variance matrices were assumed to be full rank. According to model selection criteria, the model fitting the three first principal components (PC3) provided the best fit, without the need for factor analysis models. Similar estimates of phenotypic, direct additive and maternal genetic, maternal permanent environmental and residual (co)variances were obtained with models MV and PC3. Direct heritability ranged from 0.21 (birth weight) to 0.45 (weight at 6 years of age). The genetic and phenotypic correlations obtained with model PC3 were slightly higher than those estimated with model MV. In general, the reduced-rank model substantially decreased the number of parameters in the analyses without reducing the goodness-of-fit. © 2013 Elsevier B.V.

Short communication: Principal components and factor analytic models for test-day milk yield in Brazilian Holstein cattle

A total of 46,089 individual monthly test-day (TD) milk yields (10 test-days), from 7,331 complete first lactations of Holstein cattle were analyzed. A standard multivariate analysis (MV), reduced rank analyses fitting the first 2, 3, and 4 genetic principal components (PC2, PC3, PC4), and analyses that fitted a factor analytic structure considering 2, 3, and 4 factors (FAS2, FAS3, FAS4), were carried out. The models included the random animal genetic effect and fixed effects of the contemporary groups (herd-year-month of test-day), age of cow (linear and quadratic effects), and days in milk (linear effect). The residual covariance matrix was assumed to have full rank. Moreover, 2 random regression models were applied. Variance components were estimated by restricted maximum likelihood method. The heritability estimates ranged from 0.11 to 0.24. The genetic correlation estimates between TD obtained with the PC2 model were higher than those obtained with the MV model, especially on adjacent test-days at the end of lactation close to unity. The results indicate that for the data considered in this study, only 2 principal components are required to summarize the bulk of genetic variation among the 10 traits.

A new analytic approach for power system fault diagnosis employing the temporal information of alarm messages

Traditional analytic models for power system fault diagnosis are usually formulated as an unconstrained 0–1 integer programming problem. The key issue of the models is to seek the fault hypothesis that minimizes the discrepancy between the actual and the expected states of the concerned protective relays and circuit breakers. The temporal information of alarm messages has not been well utilized in these methods, and as a result, the diagnosis results may be not unique and hence indefinite, especially when complicated and multiple faults occur. In order to solve this problem, this paper presents a novel analytic model employing the temporal information of alarm messages along with the concept of related path. The temporal relationship among the actions of protective relays and circuit breakers, and the different protection configurations in a modern power system can be reasonably represented by the developed model, and therefore, the diagnosed results will be more definite under different circumstances of faults. Finally, an actual power system fault was served to verify the proposed method.

Calibrating Analytical Models for Semilocal Strings

In this work we calibrate two different analytic models of semilocal strings by constraining the values of their free parameters. In order to do so, we use data obtained from the largest and most accurate field theory simulations of semilocal strings to date, and compare several key properties with the predictions of the models. As this is still work in progress, we present some preliminary results together with descriptions of the methodology we are using in the characterisation of semilocal string networks.

Alternative Factor Models and Heritability of the Short Leyton Obsessional Inventory-Children's Version

An alternative models framework was used to test three confirmatory factor analytic models for the Short Leyton Obsessional Inventory-Children's Version (Short LOI-CV) in a general population sample of 517 young adolescent twins (11-16 years). A one-factor model as implicit in current classification systems of Obsessive-Compulsive Disorder (OCD), a two-factor obsessions and compulsions model, and a multidimensional model corresponding to the three proposed subscales of the Short LOI-CV (labelled Obsessions/Incompleteness, Numbers/Luck and Cleanliness) were considered. The three-factor model was the only model to provide an adequate explanation of the data. Twin analyses suggested significant quantitative sex differences in heritability for both the Obsessions/Incompleteness and Numbers/Luck dimensions with these being significantly heritable in males only (heritability of 60% and 65% respectively). The correlation between the additive genetic effects for these two dimensions in males was 0.95 suggesting they largely share the same genetic risk factors.

CIMMYT-selected derived synthetic bread wheats for rainfed environments: Yield evaluation in Mexico and Australia.

Synthetic backcrossed-derived bread wheats (SBWs) from CIMMYT were grown in the Northwest of Mexico at Centro de Investigaciones Agrícolas del Noroeste (CIANO) and sites across Australia during three seasons. During three consecutive years Australia received “shipments” of different SBWs from CIMMYT for evaluation. A different set of lines was evaluated each season, as new materials became available from the CIMMYT crop enhancement program. These consisted of approximately 100 advanced lines (F7) per year. SBWs had been top and backcrossed to CIMMYT cultivars in the first two shipments and to Australian wheat cultivars in the third one. At CIANO, the SBWs were trialled under receding soil moisture conditions. We evaluated both the performance of each line across all environments and the genotype-by-environment interaction using an analysis that fits a multiplicative mixed model, adjusted for spatial field trends. Data were organised in three groups of multienvironment trials (MET) containing germplasm from shipment 1 (METShip1), 2 (METShip2), and 3 (METShip3), respectively. Large components of variance for the genotype × environment interaction were found for each MET analysis, due to the diversity of environments included and the limited replication over years (only in METShip2, lines were tested over 2 years). The average percentage of genetic variance explained by the factor analytic models with two factors was 50.3% for METShip1, 46.7% for METShip2, and 48.7% for METShip3. Yield comparison focused only on lines that were present in all locations within a METShip, or “core” SBWs. A number of core SBWs, crossed to both Australian and CIMMYT backgrounds, outperformed the local benchmark checks at sites from the northern end of the Australian wheat belt, with reduced success at more southern locations. In general, lines that succeeded in the north were different from those in the south. The moderate positive genetic correlation between CIANO and locations in the northern wheat growing region likely reflects similarities in average temperature during flowering, high evaporative demand, and a short flowering interval. We are currently studying attributes of this germplasm that may contribute to adaptation, with the aim of improving the selection process in both Mexico and Australia.

Distance dependence of fluorescence resonance energy transfer

Deviations from the usual R (-6) dependence of the rate of fluorescence resonance energy transfer (FRET) on the distance between the donor and the acceptor have been a common scenario in the recent times. In this paper, we present a critical analysis of the distance dependence of FRET, and try to illustrate the non R (-6) type behaviour of the rate for the case of transfer from a localized electronic excitation on the donor, a dye molecule to three different energy acceptors with delocalized electronic excitations namely, graphene,two-dimensional semiconducting sheet and the case of such a semiconducting sheet rolled to obtain a nanotube. We use simple analytic models to understand the distance dependence in each case.

单（多）井抽灌对浅部地温场的影响研究

The technique of energy extraction using groundwater source heat pumps, as a sustainable way of low-grade thermal energy utilization, has widely been used since mid-1990's. Based on the basic theories of groundwater flow and heat transfer and by employing two analytic models, the relationship of the thermal breakthrough time for a production well with the effect factors involved is analyzed and the impact of heat transfer by means of conduction and convection, under different groundwater velocity conditions, on geo-temperature field is discussed.A mathematical model, coupling the equations for groundwater flow with those for heat transfer, was developed. The impact of energy mining using a single well system of supplying and returning water on geo-temperature field under different hydrogeological conditions, well structures, withdraw-and-reinjection rates, and natural groundwater flow velocities was quantitatively simulated using the finite difference simulator HST3D. Theoretical analyses of the simulated results were also made. The simulated results of the single well system indicate that neither the permeability nor the porosity of a homogeneous aquifer has significant effect on the temperature of the production segment provided that the production and injection capability of each well in the aquifers involved can meet the designed value. If there exists a lower permeable interlayer, compared with the main aquifer, between the production and injection segments, the temperature changes of the production segment will decrease. The thicker the interlayer and the lower the interlayer permeability, the longer the thermal breakthrough time of the production segment and the smaller the temperature changes of the production segment. According to the above modeling, it can also be found that with the increase of the aquifer thickness, the distance between the production and injection screens, and/or the regional groundwater flow velocity, and/or the decrease of the production-and-reinjection rate, the temperature changes of the production segment decline. For an aquifer of a constant thickness, continuously increase the screen lengths of production and injection segments may lead to the decrease of the distance between the production and injection screens, and the temperature changes of the production segment will increase, consequently.According to the simulation results of the single well system, the parameters, that can cause significant influence on heat transfer as well as geo-temperature field, were chosen for doublet system simulation. It is indicated that the temperature changes of the pumping well will decrease as the aquifer thickness, the distance between the well pair and/or the screen lengths of the doublet increase. In the case of a low permeable interlayer embedding in the main aquifer, if the screens of the pumping and the injection wells are installed respectively below and above the interlayer, the temperature changes of the pumping well will be smaller than that without the interlay. The lower the permeability of the interlayer, the smaller the temperature changes. The simulation results also indicate that the lower the pumping-and-reinjection rate, the greater the temperature changes of the pumping well. It can also be found that if the producer and the injector are chosen reasonably, the temperature changes of the pumping well will decline as the regional groundwater flow velocity increases. Compared with the case that the groundwater flow direction is perpendicular to the well pair, if the regional flow is directed from the pumping well to the injection well, the temperature changes of the pumping well is relatively smaller.Based on the above simulation study, a case history was conducted using the data from an operating system in Beijing. By means of the conceptual model and the mathematical model, a 3-D simulation model was developed and the hydrogeological parameters and the thermal properties were calibrated. The calibrated model was used to predict the evolution of the geo-temperature field for the next five years. The simulation results indicate that the calibrated model can represent the hydrogeological conditions and the nature of the aquifers. It can also be found that the temperature fronts in high permeable aquifers move very fast and the radiuses of temperature influence are large. Comparatively, the temperature changes in clay layers are smaller and there is an obvious lag of the temperature changes. According to the current energy mining load, the temperature of the pumping wells will increase by 0.7°C at the end of the next five years. The above case study may provide reliable base for the scientific management of the operating system studied.

Mistreatment in Distributed Caching Groups: Causes and Implications

Although cooperation generally increases the amount of resources available to a community of nodes, thus improving individual and collective performance, it also allows for the appearance of potential mistreatment problems through the exposition of one node’s resources to others. We study such concerns by considering a group of independent, rational, self-aware nodes that cooperate using on-line caching algorithms, where the exposed resource is the storage of each node. Motivated by content networking applications – including web caching, CDNs, and P2P – this paper extends our previous work on the off-line version of the problem, which was limited to object replication and was conducted under a game-theoretic framework. We identify and investigate two causes of mistreatment: (1) cache state interactions (due to the cooperative servicing of requests) and (2) the adoption of a common scheme for cache replacement/redirection/admission policies. Using analytic models, numerical solutions of these models, as well as simulation experiments, we show that online cooperation schemes using caching are fairly robust to mistreatment caused by state interactions. When this becomes possible, the interaction through the exchange of miss-streams has to be very intense, making it feasible for the mistreated nodes to detect and react to the exploitation. This robustness ceases to exist when nodes fetch and store objects in response to remote requests, i.e., when they operate as Level-2 caches (or proxies) for other nodes. Regarding mistreatment due to a common scheme, we show that this can easily take place when the “outlier” characteristics of some of the nodes get overlooked. This finding underscores the importance of allowing cooperative caching nodes the flexibility of choosing from a diverse set of schemes to fit the peculiarities of individual nodes. To that end, we outline an emulation-based framework for the development of mistreatment-resilient distributed selfish caching schemes.

Distributed Selfish Coaching

Although cooperation generally increases the amount of resources available to a community of nodes, thus improving individual and collective performance, it also allows for the appearance of potential mistreatment problems through the exposition of one node's resources to others. We study such concerns by considering a group of independent, rational, self-aware nodes that cooperate using on-line caching algorithms, where the exposed resource is the storage at each node. Motivated by content networking applications -- including web caching, CDNs, and P2P -- this paper extends our previous work on the on-line version of the problem, which was conducted under a game-theoretic framework, and limited to object replication. We identify and investigate two causes of mistreatment: (1) cache state interactions (due to the cooperative servicing of requests) and (2) the adoption of a common scheme for cache management policies. Using analytic models, numerical solutions of these models, as well as simulation experiments, we show that on-line cooperation schemes using caching are fairly robust to mistreatment caused by state interactions. To appear in a substantial manner, the interaction through the exchange of miss-streams has to be very intense, making it feasible for the mistreated nodes to detect and react to exploitation. This robustness ceases to exist when nodes fetch and store objects in response to remote requests, i.e., when they operate as Level-2 caches (or proxies) for other nodes. Regarding mistreatment due to a common scheme, we show that this can easily take place when the "outlier" characteristics of some of the nodes get overlooked. This finding underscores the importance of allowing cooperative caching nodes the flexibility of choosing from a diverse set of schemes to fit the peculiarities of individual nodes. To that end, we outline an emulation-based framework for the development of mistreatment-resilient distributed selfish caching schemes. Our framework utilizes a simple control-theoretic approach to dynamically parameterize the cache management scheme. We show performance evaluation results that quantify the benefits from instantiating such a framework, which could be substantial under skewed demand profiles.

The development and validation of computational MHD techniques for the modelling of metal production processes

Magnetic fields are used in a number of processes related to the extraction of metals, production of alloys and the shaping of metal components. Computational techniques have an increasingly important role to play in the simulation of such processes, since it is often difficult or very costly to conduct experiments in the high temperature conditions encountered and the complex interaction of fluid flow, heat transfer and magnetic fields means simple analytic models are often far removed from reality. In this paper an overview of the computational activity at the University of Greenwich is given in this area, covering the past ten years. The overview is given from the point of view of the modeller and within the space limitations imposed by the format it covers the numerical methods used, attempts at validation against experiments or analytic procedures; it highlights successes, but also some failures. A broad range of models is covered in the review (and accompanying lecture), used to simulate (a) A-C field applications: induction melting, magnetic confinement and levitation, casting and (b) D-C field applications such as: arc welding and aluminium electroloysis. Most of these processes involve phase change of the metal (melting or solidification), the presence of a dynamic free surface and turbulent flow. These issues affect accuracy and need to be address by the modeller.